[bug#61933] [PATCH 0/9] *** A requested with 8 dependencies ***

[bug#61933] [PATCH 0/9] *** A requested with 8 dependencies ***

[Navid Afkhami]

*** A requested package, which is r-seurat-utils, that has 8 dependencies ***

Navid Afkhami (9):
  gnu: Add r-stringendo.
  gnu: Add r-readwriter.
  gnu: Add r-codeandroll2.
  gnu: Add r-markdownhelpers.
  gnu: Add r-markdownreports.
  gnu: Add r-ggexpress.
  gnu: Add r-tictoc.
  gnu: Add r-hgnchelper.
  gnu: Add r-seurat-utils.

 gnu/packages/bioinformatics.scm | 281 ++++++++++++++++++++++++++++++++
 1 file changed, 281 insertions(+)


base-commit: 4f681cdbc27e6a922f24d4297efe3c0b823195f0
-- 
2.34.1

[bug#61933] [PATCH vREVISION 1/9] gnu: Add r-stringendo.

[Navid Afkhami]

* gnu/packages/bioinformatics.scm (r-stringendo): New variable.
---
 gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 858fd1e975..caa50ce3bd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -793,6 +793,30 @@ (define-public r-rhtslib12
 developers of other R packages who wish to make use of HTSlib.")
       (license license:lgpl2.0+))))
 
+(define-public r-stringendo
+  (let ((commit "83b8f2d82a09b33b9e895438bb523a021138be01")
+        (revision "1"))
+    (package
+      (name "r-stringendo")
+      (version (git-version "0.3.4" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/Stringendo")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1ap0nhbyd6xx0yl2vgmwk38p22yrkv4k9hw13r35z4wf343rry6v"))))
+      (properties `((upstream-name . "Stringendo")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-devtools r-usethis))
+      (home-page "https://github.com/vertesy/Stringendo")
+      (synopsis "Stringendo is a string parsing library")
+      (description
+       "String parsing functionalites for generating plotnames, filenames and path.")
+      (license license:gpl3))))
+
 (define-public r-streamgraph
   (let ((commit "76f7173ec89d456ace5943a512e20b1f6810bbcb")
         (revision "1"))

base-commit: 4f681cdbc27e6a922f24d4297efe3c0b823195f0
-- 
2.34.1

[bug#61933] [PATCH vREVISION 2/9] gnu: Add r-readwriter.

[Navid Afkhami]

* gnu/packages/bioinformatics.scm (r-readwriter): New variable.
---
 gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index caa50ce3bd..42e082765e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -817,6 +817,31 @@ (define-public r-stringendo
        "String parsing functionalites for generating plotnames, filenames and path.")
       (license license:gpl3))))
 
+(define-public r-readwriter
+  (let ((commit "71454f4aa706f5d2fbe606acd95abc14224e7058")
+        (revision "1"))
+    (package
+      (name "r-readwriter")
+      (version (git-version "0.2.9" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/ReadWriter")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0sp27smhdva2hi2x0svia2l56k8xrh7p5akn78g5b0lcvz4x3hd7"))))
+      (properties `((upstream-name . "ReadWriter")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-gdata r-gtools r-openxlsx r-readr
+                               r-stringendo))
+      (home-page "https://github.com/vertesy/ReadWriter")
+      (synopsis "Functions to read and write files conveniently")
+      (description
+       "ReadWriter is a set of R functions to read and write files conveniently.")
+      (license license:gpl3))))
+
 (define-public r-streamgraph
   (let ((commit "76f7173ec89d456ace5943a512e20b1f6810bbcb")
         (revision "1"))
-- 
2.34.1

[bug#61933] [PATCH vREVISION 3/9] gnu: Add r-codeandroll2.

[Navid Afkhami]

* gnu/packages/bioinformatics.scm (r-codeandroll2): New variable.
---
 gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 42e082765e..fdfbf6459b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -719,6 +719,40 @@ (define-public r-btools
 for all types of microbial diversity analyses.")
       (license license:expat))))
 
+(define-public r-codeandroll2
+  (let ((commit "d58e258851a5c0b430e8620d34dbeefb597c548f")
+        (revision "1"))
+    (package
+      (name "r-codeandroll2")
+      (version (git-version "2.3.6" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/CodeAndRoll2")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0sy88mfgw6qqhpnlc5020qzr1jllkcrxfhl2lw42bkl5nb56is71"))))
+      (properties `((upstream-name . "CodeAndRoll2")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-colorramps
+                               r-dplyr
+                               r-gplots
+                               r-gtools
+                               r-plyr
+                               r-rcolorbrewer
+                               r-sessioninfo
+                               r-sm
+                               r-stringendo
+                               r-stringr))
+      (home-page "https://github.com/vertesy/CodeAndRoll2")
+      (synopsis "CodeAndRoll2 for vector, matrix and list manipulations")
+      (description
+       "CodeAndRoll2 is a set of more than 130 productivity functions.
+These functions are used by MarkdownReports, ggExpress, SeuratUtils.")
+      (license license:gpl3))))
+
 (define-public r-conospanel
   (let ((commit "39e76b201a783b4e92fd615010a735a61746fbb9")
         (revision "1"))
-- 
2.34.1

[bug#61933] [PATCH vREVISION 4/9] gnu: Add r-markdownhelpers.

[Navid Afkhami]

* gnu/packages/bioinformatics.scm (r-markdownhelpers): New variable.
---
 gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fdfbf6459b..c6c0da74ff 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8813,6 +8813,30 @@ (define-public r-sccustomize
 visualization and analysis of single-cell data using R.")
       (license license:gpl3+))))
 
+(define-public r-markdownhelpers
+  (let ((commit "793372d28ebed607cc1d35f909a1caedb2b41ffe")
+        (revision "1"))
+    (package
+      (name "r-markdownhelpers")
+      (version (git-version "0.2.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/MarkdownHelpers")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1d18s2ydhfjm3hjkxz42dirhwrrv792m6mvkmypallaa2qnwrmkg"))))
+      (properties `((upstream-name . "MarkdownHelpers")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-devtools r-stringendo r-usethis))
+      (home-page "https://github.com/vertesy/MarkdownHelpers")
+      (synopsis "Helper functions for MarkdownReports and ggExpress")
+      (description
+       "Set of R functions to parse markdown and other generic helpers.")
+      (license license:gpl3))))
+
 (define-public r-snapatac
   (package
     (name "r-snapatac")
-- 
2.34.1

[bug#61933] [PATCH vREVISION 5/9] gnu: Add r-markdownreports.

[Navid Afkhami]

* gnu/packages/bioinformatics.scm (r-markdownreports): New variable.
---
 gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c6c0da74ff..b311ec6c33 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8837,6 +8837,43 @@ (define-public r-markdownhelpers
        "Set of R functions to parse markdown and other generic helpers.")
       (license license:gpl3))))
 
+(define-public r-markdownreports
+  (let ((commit "3ba1103e3ddc6df3a0c090eb884f5e65c461eb31")
+        (revision "1"))
+    (package
+      (name "r-markdownreports")
+      (version (git-version "4.5.9" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/MarkdownReports")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1xmasdb630b6nvxi5m1i8pyxiy49nxpzyxf9h8spdppx92rhdkc8"))))
+      (properties `((upstream-name . "MarkdownReports")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-clipr
+                               r-codeandroll2
+                               r-colorramps
+                               r-devtools
+                               r-gplots
+                               r-markdownhelpers
+                               r-rcolorbrewer
+                               r-readwriter
+                               r-sessioninfo
+                               r-sm
+                               r-stringendo
+                               r-venndiagram
+                               r-vioplot))
+      (home-page "https://github.com/vertesy/MarkdownReports")
+      (synopsis "Tool for generating cientific figures and reports")
+      (description
+       "This is a set of R functions that allows you to generate precise figures.
+This tool will create clean markdown reports about what you just discovered.")
+      (license license:gpl3))))
+
 (define-public r-snapatac
   (package
     (name "r-snapatac")
-- 
2.34.1

[bug#61933] [PATCH vREVISION 6/9] gnu: Add r-ggexpress.

[Navid Afkhami]

* gnu/packages/bioinformatics.scm (r-ggexpress): New variable.
---
 gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b311ec6c33..14efaa9570 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8302,6 +8302,43 @@ (define-public infernal
     (supported-systems '("i686-linux" "x86_64-linux"))
     (license license:bsd-3)))
 
+(define-public r-ggexpress
+  (let ((commit "82f169385f87af328ff971195c2f64ff3c573a8a")
+        (revision "1"))
+    (package
+      (name "r-ggexpress")
+      (version (git-version "0.6.6" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/ggExpress")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "122hnw8xv33ngcd4fd7hmf817a06ih1knrxxi0cgklj1fwinm0z4"))))
+      (properties `((upstream-name . "ggExpress")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-cowplot
+                               r-ggplot2
+                               r-ggpubr
+                               r-markdownhelpers
+                               r-markdownreports
+                               r-rcolorbrewer
+                               r-sessioninfo
+                               r-seurat
+                               r-sm
+                               r-stringendo
+                               r-tidyverse))
+      (home-page "https://github.com/vertesy/ggExpress")
+      (synopsis
+       "This is a fast tool to create, annotate and export plots in R")
+      (description
+       "This package is a set of R functions for generating precise figures.
+This tool helps you to create clean markdown reports about what you just
+discovered with your analysis script.")
+      (license license:gpl3))))
+
 (define-public r-gg3d
   (let ((commit "ffdd837d30c1671cd0895db94bdd7b1594dbfcb0")
         (revision "1"))
-- 
2.34.1

[bug#61933] [PATCH vREVISION 7/9] gnu: Add r-tictoc.

[Navid Afkhami]

* gnu/packages/bioinformatics.scm (r-tictoc): New variable.
---
 gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 14efaa9570..42d0923ab1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8960,6 +8960,28 @@ (define-public r-snapatac
 single cell ATAC-seq sequencing data.")
     (license license:gpl3)))
 
+(define-public r-tictoc
+  (package
+    (name "r-tictoc")
+    (version "1.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "tictoc" version))
+              (sha256
+               (base32
+                "0ka7zd857xfqb5afn0psn0yzfv2qjb0ddxfyiq6aggbnla5qc3qj"))))
+    (properties `((upstream-name . "tictoc")))
+    (build-system r-build-system)
+    (home-page "https://github.com/jabiru/tictoc")
+    (synopsis
+     "Functions for timing R scripts and implementations of stack and list structures")
+    (description
+     "The tictoc package provides the timing functions tic and toc that can be nested.
+It provides an alternative to @code{system.time()} with a different syntax similar to
+that in another well-known software package. tic and toc are easy to use, and are
+especially useful when timing several sections in more than a few lines of code.")
+    (license license:asl2.0)))
+
 (define-public r-tsis
   (let ((commit "24460298fbe1d26e4da390f6e4f3d4d9d62334dc")
         (revision "1"))
-- 
2.34.1

[bug#61933] [PATCH vREVISION 8/9] gnu: Add r-hgnchelper.

[Navid Afkhami]

* gnu/packages/bioinformatics.scm (r-hgnchelper): New variable.
---
 gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 42d0923ab1..b179fcb61a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9139,6 +9139,29 @@ (define-public r-archr
        "This package is designed to streamline scATAC analyses in R.")
       (license license:gpl2+))))
 
+(define-public r-hgnchelper
+  (package
+    (name "r-hgnchelper")
+    (version "0.8.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "HGNChelper" version))
+              (sha256
+               (base32
+                "0qwkk5658j4j6w2wgvxkp38cyvscjp93d3zc7gb97vcihqx0ngxa"))))
+    (properties `((upstream-name . "HGNChelper")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/waldronlab/HGNChelper")
+    (synopsis
+     "Identification and correction of invalid gene symbols for human and mouse")
+    (description
+     "Set of R functions for identifying and correcting HGNC human gene symbols.
+In addition, you can identify MGI mouse gene symbols, which have been converted
+to date format by Excel, withdrawn, or aliased.  Also contains functions for
+reversibly converting between HGNC symbols and valid R names.")
+    (license license:gpl2+)))
+
 (define-public r-icellnet
   ;; v1.0 tagged in 2020, last commit contains many fixes.
   ;; DESCRIPTION says Version: 0.0.0.9000.
-- 
2.34.1

[bug#61933] [PATCH vREVISION 9/9] gnu: Add r-seurat-utils.

[Navid Afkhami]

* gnu/packages/bioinformatics.scm (r-seurat-utils): New variable.
---
 gnu/packages/bioinformatics.scm | 55 +++++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b179fcb61a..31dd2d856f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15955,6 +15955,61 @@ (define-public r-scopeloomr
 files.")
       (license license:expat))))
 
+(define-public r-seurat-utils
+  (let ((commit "0b6f5b548a49148cfbeaa654e8a618c0a020afa5")
+        (revision "1"))
+    (package
+      (name "r-seurat-utils")
+      (version (git-version "1.6.5" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/Seurat.utils")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1mn64h375mkj6x4ix5493z32gqg96yc507j5jr0lx9g5wk1bf762"))))
+      (properties `((upstream-name . "Seurat.utils")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-codeandroll2
+                               r-cowplot
+                               r-dplyr
+                               r-ggcorrplot
+                               r-ggexpress
+                               r-ggplot2
+                               r-ggpubr
+                               r-ggrepel
+                               r-hgnchelper
+                               r-htmlwidgets
+                               r-markdownhelpers
+                               r-markdownreports
+                               r-matrix
+                               r-matrixstats
+                               r-princurve
+                               r-r-utils
+                               r-readr
+                               r-readwriter
+                               r-reshape2
+                               r-scales
+                               r-seurat
+                               r-soupx
+                               r-sparsematrixstats
+                               r-stringendo
+                               r-stringr
+                               r-tibble
+                               r-tictoc
+                               r-vroom))
+      (home-page "https://github.com/vertesy/Seurat.utils")
+      (synopsis "Seurat.utils is a collection of utility functions for Seurat")
+      (description
+       "This is a collection of utility functions for Seurat v3.
+These Functions allow the automation and  multiplexing of plotting,
+3D plotting, visualisation of statistics & QC, interaction with the
+Seurat object.  Some functionalities require functions from
+CodeAndRoll and MarkdownReports libraries.")
+      (license license:gpl3))))
+
 (define-public r-seuratwrappers
   ;; There are no releases or tags.
   (let ((commit "d28512f804d5fe05e6d68900ca9221020d52cf1d")
-- 
2.34.1

bug#61933: [PATCH 0/9] *** A requested with 8 dependencies ***

[Ricardo Wurmus]

Thank you for the patches.  I applied them all with minor changes to the
descriptions.

-- 
Ricardo